To load 10x data there a several options with pros an cons.
## [1] "Gzma" "Ccl4" "Ifitm1" "Trbv17" "Ccl1" "Penk"
## [7] "Hbb-bs" "Hba-a1" "Ecm1" "Areg" "Cxcl2" "Gcg"
## [13] "Hba-a2" "Cxcl10" "Trbv1" "Ccl3" "Trbv15" "Hbb-bt"
## [19] "Trbv29" "Trav8d-2"
## PC_ 1
## Positive: Vps37b, Bhlhe40, Ifrd1, Tnfaip3, Hilpda
## Negative: Rps8, Rps20, Rpl28, Rpl10a, Ifi47
## PC_ 2
## Positive: AW112010, Ifi27l2a, Ly6a, S100a11, Cxcr3
## Negative: Rpl13, Rps2, Rpl32, Rps5, Igfbp4
## PC_ 3
## Positive: Birc5, Stmn1, Pclaf, Ccna2, Spc24
## Negative: Rpl13, Rps4x, Rps5, Rps18, Rpl8
## PC_ 4
## Positive: S100a6, Vim, Lgals3, Nkg7, Crip1
## Negative: Izumo1r, Stat1, Cd74, Cd81, Cd83
## PC_ 5
## Positive: Lgals1, Vim, Actg1, S100a10, S100a6
## Negative: Zfp36l2, Jun, Evl, Cd7, Btg2
## 2C_AAACCTGAGTCGAGTG-1 2C_AAACCTGCAGCCAGAA-1 2C_AAACCTGCAGGGCATA-1
## 0 0 0
## 2C_AAACCTGCATTTCAGG-1 2C_AAACCTGGTCGCTTCT-1
## 0 0
## Levels: 0 1 2 3 4 5 6 7 8 9 10 11 12
There are some cluster with higher ribosomal gene percentage in clusters 3,6,11 and 12. Cluster 3(12) is a rather spleen specific cluster, while 6 (11) are input cells. The number of counts per cell is especially high in 5,8 (liver/spleen) and